There several cases when you may want to abandon a colony. Easing border tension is one. Maybe you want to create a no man's land between you and a other empire. Maybe one of the planets was a conquered one and vasalization is not the best option. Maybe it is a tomb world you inherited (or accentually colonized) and you do not want to piss off you religious pop or a religious empire. Maybe you want to make you empire more lean and focus more on building tall avoiding those low pop planets. Maybe you want to avoid the planet falling in the the wrong hands. (This last situation however must be tempered with the fact that you can not instantly abandon a planet. You can already gift the planet to someone else to avoid that it falls in rival already. And that is instant.)

These are some of the situations I have come by when I play where abandoning a colony have made sense.